Once 4.1 is released and I can JB my iPhone 4 (came stock with 4.0.2), I'd like to transfer my save files from my games to the other phone. There doesn't seem to be a way to do this in iTunes (only the programs transfer, not the saves). Is there some Cydia or RockApp to back it up (I have a JB'd 3GS I'm playing on right now)?

There's AppBackup. You can backup all your saves, SSH into /var/mobile/Library/Preferences/ and backup the AppBackup folder onto your computer. Then on your other device, SSH the folder back into the same directory and restore all.

But can't you just "Restore from backup" in itunes from your 3GS back up to your iPhone 4 and get all your games saved data anyway?

ya, unless you plan to keep both the iDevices with you, you should simply restore the new iPhone with your old backup. But if you do plan to keep both devices and dont want to delete the saves from the old one, you'll have to use appbackup only.

It does transfer save data. You'll have to restore the new iPhone with the old iPhone backup. iTunes asks you to choose if you want it as a new iphone or restore from an old backup. Select the latest backup of your old iPhone you can see there and you'll be good to go.

There's AppBackup. You can backup all your saves, SSH into /var/mobile/Library/Preferences/ and backup the AppBackup folder onto your computer. Then on your other device, SSH the folder back into the same directory and restore all.

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